Phylogenomics of darkling beetles (Coleoptera: Tenebrionidae) from the Atacama Desert

Background

Tenebrionidae (Insecta: Coleoptera) are a conspicuous component of desert fauna worldwide. In these ecosystems, they are significantly responsible for nutrient cycling and show remarkable morphological and physiological adaptations. Nevertheless, Tenebrionidae colonizing individual deserts have repeatedly emerged from different lineages. The goal of our study was to gain insights into the phylogenetic relationships of the tenebrionid genera from the Atacama Desert and how these taxa are related to the globally distributed Tenebrionidae.

Methods

We used newly generated transcriptome data (47 tribes, 7 of 11 subfamilies) that allowed for a comprehensive phylogenomic analysis of the tenebrionid fauna of this hyperarid desert and fills a gap in our knowledge of the highly diversified Tenebrionidae. We examined two independent data sets known to be suitable for phylogenomic reconstructions. One is based on 35 neuropeptide precursors, the other on 1,742 orthologous genes shared among Coleoptera.

Results

The majority of Atacama genera are placed into three groups, two of which belong to typical South American lineages within the Pimeliinae. While the data support the monophyly of the Physogasterini, Nycteliini and Scotobiini, this does not hold for the Atacama genera of Edrotini, Epitragini, Evaniosomini, Praociini, Stenosini, Thinobatini, and Trilobocarini. A suggested very close relationship of Psammetichus with the Mediterranean Leptoderis also could not be confirmed. We also provide hints regarding the phylogenetic relationships of the Caenocrypticini, which occur both in South America and southern Africa. Apart from the focus on the Tenebrionidae from the Atacama Desert, we found a striking synapomorphy grouping Alleculinae, Blaptinae, Diaperinae, Stenochinae, and several taxa of Tenebrioninae, but not Tenebrio and Tribolium. This character, an insertion in the myosuppressin gene, defines a higher-level monophyletic group within the Tenebrionidae.

Conclusion

Transcriptome data allow a comprehensive phylogenomic analysis of the tenebrionid fauna of the Atacama Desert, which represents one of the seven major endemic tribal areas in the world for Tenebrionidae. Most Atacama genera could be placed in three lineages typical of South America; monophyly is not supported for several tribes based on molecular data, suggesting that a detailed systematic revision of several groups is necessary.

Mass Spectrometric Proof of Predicted Peptides: Novel Adipokinetic Hormones in Insects

The importance of insects in our ecosystems is undeniable. The indiscriminate use of broad-spectrum insecticides is a factor in the decline in insect biomass. We identify and sequence a prominent neuropeptide hormone in insects with an overarching goal to elucidate relatedness and create a database of bioactive peptides that could inform possible cross-activity in biological assays for the identification of a biorational lead compound. The major task of an adipokinetic hormone (AKH) in an insect is the regulation of metabolic events, such as carbohydrate and lipid breakdown in storage tissue during intense muscular work. From genomic and/or transcriptomic information one may predict the genes encoding neuropeptides such as the AKHs of insects. Definite elucidation of the primary structure of the mature peptide with putative post-translational modifications needs analytical chemical methods. Here we use high-resolution mass spectrometry coupled with liquid chromatography to identify unequivocally the AKHs of five insect species (one cockroach, two moths, and two flies) of which either genomic/transcriptomic information was available or sequences from related species. We confirm predicted sequences and discover novel AKH sequences, including one with a post-translational hydroxyproline modification. The additional sequences affirm an evolutionary pattern of dipteran AKHs and a conserved pattern in crambid moths.

Hidden Diversity—A New Speciose Gall Midge Genus (Diptera: Cecidomyiidae) Associated with Succulent Aizoaceae in South Africa

Simple Summary

Succulent Aizoaceae (often called “mesembs” or ice plants) form a dominant component of the Succulent Karoo in southern Africa, constituting one of the most species-rich families within the Greater Cape Floristic Region (GCFR). Despite the diversity and abundance of these plants, the diversity of insects specialized on them has never been surveyed methodically prior to this study. In a three-year study of the galling insects associated with succulent Aizoaceae in South Africa, we found that they support a rich community of gall midges (Diptera: Cecidomyiidae), virtually all of which are new to science. This is not surprising, given that knowledge of the Afrotropical fauna of gall midges is scarce, with most species described in the 1900s. Here, we describe the new genus Ruschiola with ten species from succulent Aizoaceae in Namaqualand, the Knersvlakte and the Cedarberg regions of South Africa based on morphological, molecular and life history data. The genetic data were particularly important in this study for differentiating taxa, given that Ruschiola species are very similar morphologically. Members of this genus develop in leaf galls or in plant tissues without visible gall formation, and are highly host specific.

Abstract

Aizoaceae (Caryophyllales) constitute one of the major floral components of the unique Greater Cape Floristic Region (GCFR), with more than 1700 species and 70% endemism. Within succulent Aizoaceae, the subfamily Ruschioideae is the most speciose and rapidly diversifying clade, offering potential niches for the diversification of specialized herbivorous insects. Nevertheless, insect diversity on these plants has not been studied to date, and knowledge of gall-inducing insects in the Afrotropics is generally scarce. Our recent observations indicate that succulent Aizoaceae in the GCFR support a rich and largely unstudied community of gall midges (Diptera: Cecidomyiidae). Here, we provide a first report of their diversity with a description of a new genus, Ruschiola Dorchin, and ten new species, based on morphological and molecular analyses of material collected during a three-year targeted survey across major GCFR vegetation types. A high degree of morphological uniformity in Ruschiola suggests recent diversification and necessitated the use of molecular data and laboratory rearing from host plants to verify species boundaries and host ranges.

Expression pattern of CAPA/pyrokinin neuropeptide genes in Remipedia and silverfish: Rapid differentiation after gene duplication in early Hexapoda, followed by strong conservation of newly established features in insects

Only few genes are known from insects that encode multiple neuropeptides, i.e., peptides that activate different receptors. Among those are the capa and pk genes, which differentiated within Hexapoda following gene duplication. In our study, we focus on the early stages of differentiation of these genes. Specifically: (1) What was the expression pattern of the ancestral capa/pk gene, i.e., prior to gene duplication? (2) What is the expression pattern of capa and pk in silverfish, whose ancestors diverged from Pterygota more than 400 mya? Our results suggest the location and projection of CAPA immunoreactive Va cells in abdominal ganglia (trunk ganglia in Remipedia) are a plesiomorphic trait that was already present in the ancestor of Remipedia and Hexapoda. General features of serial homology such as location of cells bodies, contralateral projection of primary neurites, and presumed peripheral peptide release from segmentally arranged neurohemal release sites could be observed in Remipedia and silverfish, but also in all Pterygota studied so far. Differences are mainly in the specific location of these peripheral release sites. This hypothetical basic pattern of capa/pk neurons underwent modifications in the anterior ganglia of the ventral nerve cord already in Remipedia. In silverfish, as in all Pterygota studied so far, pk expression in the CNS is apparently restricted to the gnathal ganglia, whereas capa expression is typical of abdominal Va cells. Thus, differentiation in the expression pattern of capa and pk genes occurred early in the evolution of Hexapoda; likely soon after the appearance of two separate genes.

Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage

Key changes in ecological niche space are often critical to understanding how lineages diversify during adaptive radiations. However, the converse, or understanding why some lineages are depauperate and relictual, is more challenging, as many factors may constrain niche evolution. In the case of the insect order Grylloblattodea, highly conserved thermal breadth is assumed to be closely tied to their relictual status, but has not been formerly tested. Here, we investigate whether evolutionary constraints in the physiological tolerance of temperature can help explain relictualism in this lineage. Using a comparative transcriptomics approach, we investigate gene expression following acute heat and cold stress across members of Grylloblattodea and their sister group, Mantophasmatodea. We additionally examine patterns of protein evolution, to identify candidate genes of positive selection. We demonstrate that cold specialization in Grylloblattodea has been accompanied by the loss of the inducible heat shock response under both acute heat and cold stress. Additionally, there is widespread evidence of selection on protein-coding genes consistent with evolutionary constraints due to cold specialization. This includes positive selection on genes involved in trehalose transport, metabolic function, mitochondrial function, oxygen reduction, oxidative stress, and protein synthesis. These patterns of molecular adaptation suggest that Grylloblattodea have undergone evolutionary trade-offs to survive in cold habitats and should be considered highly vulnerable to climate change. Finally, our transcriptomic data provide a robust backbone phylogeny for generic relationships within Grylloblattodea and Mantophasmatodea. Major phylogenetic splits in each group relate to arid conditions driving biogeographical patterns, with support for a sister-group relationship between North American Grylloblatta and Altai-Sayan Grylloblattella, and a range disjunction in Namibia splitting major clades within Mantophasmatodea.

The neuropeptidome of Carabus (Coleoptera, Adephaga: Carabidae)

Neuropeptides are signaling molecules involved in the regulation of virtually all physiological functions of Metazoa. In insects, more than 50 neuropeptide genes can be present in a single species, and thus neuropeptidergic systems are attractive targets for the development of environmentally friendly pesticides. Such approaches require not only knowledge of the neuropeptidomes of pests, but also detailed knowledge of the corresponding systems in beneficial insects. In Coleoptera, there is no profound knowledge of the neuropeptides in the adephagan lineage, which contains many of the ecologically important predators of caterpillars. We analyzed by transcriptomics, mass spectrometry and immunohistochemistry the neuropeptidomes of the two Carabus species C. violaceus and C. problematicus. This information, which contains detailed data on the differential processing of CAPA peptides, allows for the recognition of features typical only of the polyphagan lineage with its many pests. The neuropeptidomics data, which also confirmed the processing of a number of protein hormones, represent the highest number of neuropeptides that have been identified so far from Coleoptera. The sequences of the mature neuropeptides of the two Carabus species, whose ancestors separated about 13 Mya, are highly similar and no sequence substitutions were found in single-copy neuropeptides.

Evolution of Neuropeptide Precursors in Polyneoptera (Insecta)

Neuropeptides are among the structurally most diverse signaling molecules and participate in intercellular information transfer from neurotransmission to intrinsic or extrinsic neuromodulation. Many of the peptidergic systems have a very ancient origin that can be traced back to the early evolution of the Metazoa. In recent years, new insights into the evolution of these peptidergic systems resulted from the increasing availability of genome and transcriptome data which facilitated the investigation of the complete neuropeptide precursor sequences. Here we used a comprehensive transcriptome dataset of about 200 species from the 1KITE initiative to study the evolution of single-copy neuropeptide precursors in Polyneoptera. This group comprises well-known orders such as cockroaches, termites, locusts, and stick insects. Due to their phylogenetic position within the insects and the large number of old lineages, these insects are ideal candidates for studying the evolution of insect neuropeptides and their precursors. Our analyses include the orthologs of 21 single-copy neuropeptide precursors, namely ACP, allatotropin, AST-CC, AST-CCC, CCAP, CCHamide-1 and 2, CNMamide, corazonin, CRF-DH, CT-DH, elevenin, HanSolin, NPF-1 and 2, MS, proctolin, RFLamide, SIFamide, sNPF, and trissin. Based on the sequences obtained, the degree of sequence conservation between and within the different polyneopteran lineages is discussed. Furthermore, the data are used to postulate the individual neuropeptide sequences that were present at the time of the insect emergence more than 400 million years ago. The data confirm that the extent of sequence conservation across Polyneoptera is remarkably different between the different neuropeptides. Furthermore, the average evolutionary distance for the single-copy neuropeptides differs significantly between the polyneopteran orders. Nonetheless, the single-copy neuropeptide precursors of the Polyneoptera show a relatively high degree of sequence conservation. Basic features of these precursors in this very heterogeneous insect group are explained here in detail for the first time.

The power of neuropeptide precursor sequences to reveal phylogenetic relationships in insects: A case study on Blattodea

Recent state-of-the-art analyses in insect phylogeny have exclusively used very large datasets to elucidate higher-level phylogenies. We have tested an alternative and novel approach by evaluating the potential phylogenetic signals of identified and relatively short neuropeptide precursor sequences with highly conserved functional units. For that purpose, we examined available transcriptomes of 40 blattodean species for the translated amino acid sequences of 17 neuropeptide precursors. Recently proposed intra-ordinal relationships of Blattodea, based on the analysis of 2370 protein-coding nuclear single-copy genes (Evangelista et al., 2019), were corroborated with maximum support. The functionally different precursor units were analyzed separately for their phylogenetic information. Although the degree of information was different in the different sequence motifs, all precursor units contained phylogenetic informative data at the ordinal level, and their separate analysis did not reveal contradictory topologies. This study is the first comprehensive exploitation of complete neuropeptide precursor sequences of arthropods in such a context and demonstrates the applicability of these rather short but conserved sequences for an alternative, fast and simple analysis of phylogenetic relationships.

Mantophasmatodea from the Richtersveld in South Africa with description of two new genera and species

Two new species and two new genera (Kuboesphasma, Minutophasma) of Mantophasmatodea that occur in the Richtersveld region of South Africa are described. Kuboesphasma compactumgen. n., sp. n. was found only in a small area near the village of Kuboes, while Minutophasma richtersveldensegen. n., sp. n. apparently inhabits a larger area in the Richtersveld. With these two new species, a total of four different mantophasmatodeans are known to live in this area. This is a remarkable exception to the remaining representatives of this order, where even a common occurrence of only two species is rare. We discuss this sympatry in the context of the phylogeny of the group. Additionally, we provide a map of the known distributions and a table with the most important taxonomic features of the mantophasmatodeans in the Richtersveld.

In silico prediction of neuropeptides in Hymenoptera parasitoid wasps

Parasitoid wasps of the order Hymenoptera, the most diverse groups of animals, are important natural enemies of arthropod hosts in natural ecosystems and can be used in biological control. To date, only one neuropeptidome of a parasitoid wasp, Nasonia vitripennis, has been identified. This study aimed to identify more neuropeptides of parasitoid wasps, by using a well-established workflow that was previously adopted for predicting insect neuropeptide sequences. Based on publicly accessible databases, totally 517 neuropeptide precursors from 24 parasitoid wasp species were identified; these included five neuropeptides (CNMamide, FMRFamide-like, ITG-like, ion transport peptide-like and orcokinin B) that were identified for the first time in parasitoid wasps, to our knowledge. Next, these neuropeptides from parasitoid wasps were compared with those from other insect species. Phylogenetic analysis suggested the divergence of AST-CCC within Hymenoptera. Further, the encoding patterns of CAPA/PK family genes were found to be different between Hymenoptera species and other insect species. Some neuropeptides that were not found in some parasitoid superfamilies (e.g., sulfakinin), or considerably divergent between different parasitoid superfamilies (e.g., sNPF) might be related to distinct physiological processes in the parasitoid life. Information of neuropeptide sequences in parasitoid wasps can be useful for better understanding the phylogenetic relationships of Hymenoptera and further elucidating the physiological functions of neuropeptide signaling systems in parasitoid wasps.

Identification of mature peptides from pban and capa genes of the moths Heliothis peltigera and Spodoptera littoralis

By transcriptome analysis, we identified PBAN and CAPA precursors in the moths Spodoptera littoralis and Heliothis peltigera which are among the most damaging pests of agriculture in tropical and subtropical Africa as well as in Mediterranean countries. A combination of mass spectrometry and immunocytochemistry was used to identify mature peptides processed from these precursors and to reveal their spatial distribution in the CNS. We found that the sites of expression of pban genes, the structure of PBAN precursors and the processed neuropeptides are very similar in noctuid moths. The sequence of the diapause hormone (DH; tryptopyrokinin following the signal peptide), however, contains two N-terminal amino acids more than expected from comparison with already published sequences of related species. Capa genes of S. littoralis and H. peltigera encode, in addition to periviscerokinins, a tryptopyrokinin showing sequence similarity with DH, which is the tryptopyrokinin of the pban gene. CAPA peptides, which were not known from any noctuid moth so far, are produced in cells of abdominal ganglia. The shape of the release sites of these hormones in H. peltigera represents an exceptionally derived trait state and does not resemble the well-structured abdominal perisympathetic organs which are known from many other insects. Instead, axons of CAPA cells extensively ramify within the ventral diaphragm. The novel information regarding the sequences of all mature peptides derived from pban and capa genes of H. peltigera and S. littoralis now enables a detailed analysis of the bioactivity and species-specificity of the native peptides, especially those from the hitherto unknown capa genes, and to explore their interactions with PBAN/DH receptors.

Progress, pitfalls and parallel universes: a history of insect phylogenetics

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

Emerging tools for identification of arthropod vectors

The rapid and reliable identification of arthropod vector species is an essential component of the fight against vector-borne diseases. However, owing to the lack of entomological expertise required for the morphological identification method, development of alternative and complementary tools is needed. This review describes the main methods used for arthropod identification, focusing on the emergence of protein profiling using MALDI-TOF MS technology. Sample preparation, analysis of reproducibility, database creation and blind tests for controlling accuracy of this tool for arthropod identification are described. The advantages and limitations of the MALDI-TOF MS method are illustrated by emphasizing different hematophagous arthropods, including mosquitoes and ticks, the top two main vectors of infectious diseases.

Functional neuropeptidomics in invertebrates

Neuropeptides are key messengers in almost all physiological processes. They originate from larger precursors and are extensively processed to become bioactive. Neuropeptidomics aims to comprehensively identify the collection of neuropeptides in an organism, organ, tissue or cell. The neuropeptidome of several invertebrates is thoroughly explored since they are important model organisms (and models for human diseases), disease vectors and pest species. The charting of the neuropeptidome is the first step towards understanding peptidergic signaling. This review will first discuss the latest developments in exploring the neuropeptidome. The physiological roles and modes of action of neuropeptides can be explored in two ways, which are largely orthogonal and therefore complementary. The first way consists of inferring the functions of neuropeptides by a forward approach where neuropeptide profiles are compared under different physiological conditions. Second is the reverse approach were neuropeptide collections are used to screen for receptor-binding. This is followed by localization studies and functional tests. This review will focus on how these different functional screening methods contributed to the field of invertebrate neuropeptidomics and expanded our knowledge of peptidergic signaling. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.

Two new genera and two new species of Mantophasmatodea (Insecta, Polyneoptera) from Namibia

Two new species and two new genera (Pachyphasma, Striatophasma) of Mantophasmatodea are described from Namibia. Pachyphasma brandbergense is endemic to the Brandberg massif; Striatophasma occupies an extensive area south of the region inhabited by Mantophasma. Phylogenetic analyses (see Predel et al. in press) suggest a sistergroup relationship of Striatophasma and the South African Austrophasmatidae.